[med-svn] r3973 - in trunk/packages/mummer/trunk/debian: . patches
Charles Plessy
plessy at alioth.debian.org
Wed Sep 16 05:21:01 UTC 2009
Author: plessy
Date: 2009-09-16 05:21:00 +0000 (Wed, 16 Sep 2009)
New Revision: 3973
Added:
trunk/packages/mummer/trunk/debian/upstream-metadata.yaml
Removed:
trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff
Modified:
trunk/packages/mummer/trunk/debian/changelog
trunk/packages/mummer/trunk/debian/control
trunk/packages/mummer/trunk/debian/copyright
trunk/packages/mummer/trunk/debian/patches/02at_docs_web.diff
trunk/packages/mummer/trunk/debian/patches/series
Log:
New upstream release obsoleting debian/patches/01sm_src_tigr.diff.
Modified: trunk/packages/mummer/trunk/debian/changelog
===================================================================
--- trunk/packages/mummer/trunk/debian/changelog 2009-09-15 13:22:54 UTC (rev 3972)
+++ trunk/packages/mummer/trunk/debian/changelog 2009-09-16 05:21:00 UTC (rev 3973)
@@ -1,12 +1,20 @@
-mummer (3.21~dfsg-1) UNRELEASED; urgency=low
+mummer (3.22~dfsg-1) UNRELEASED; urgency=low
- TODO: restore the renaming, and make debian/copyright compliant with Policy.
+ TODO: restore the renaming
- * New upstream release (GCC compatibility fix.)
+ * New upstream release:
+ 3.22
+ - Significant 'dnadiff' bug fixes.
+ - Unaligned contig output format switched to match show-diff format.
+ - Dynamic memory allocation for run-mummer1.
+ - Turned off output of the near useless .cluster files from nucmer and
+ promer (let us know if you still want them).
+ 3.21
+ - gcc compatability fix.
* debian/get-orig-source: rename mutilated upstream tarball.
* debian/control:
- incremented Standards-Version to reflect concordance with Debian Policy
- 3.8.2 (no changes needed).
+ 3.8.3 (no changes needed).
- mummer-docs depends on ${misc:Depends}.
- dropped versionned dependencies when they are even satisfied in oldstable.
- dropped dependency on CDBS and patchutils, and added dependency on quilt.
@@ -15,17 +23,21 @@
- replaces some Makefile patches by environment variables in debian/rules.
- replaced 02at_scripts.diff by separate files in sh-replacement-scripts.
- added a series file to use Quilt.
- - refreshed the patch ‘01sm_src_tigr.diff’ that allows to use MUMmer on
- computers with less that 512 Mo of memory, with the great help of
- Boyd Stephen Smith Jr.
+ - dropped the patch ‘01sm_src_tigr.diff’ that allowed to use MUMmer on
+ computers with less that 512 Mo of memory and is now obsoleted by
+ this release.
+ - refreshed the 02at_docs_web.diff patch that redirects the links for the
+ suppressed PDF files to the upstream website.
* debian/rules converted to debhelper (the build system is too odd to be
handled gently by CDBS without patches).
* Mangled ‘~dfsg’ from the Debian version number in debian/watch.
* Converted debian/copyright to a machine-readable format.
* Documented the PDF deletion and the patching in ‘debian/README.source’.
* Turned the get-orig-source shell script into a debian/rule target.
+ * Added an experimental collection of upstream metadata in YAML format
+ (debian/upstream-metadata.yaml).
- -- Charles Plessy <plessy at debian.org> Mon, 13 Jul 2009 08:30:24 +0900
+ -- Charles Plessy <plessy at debian.org> Wed, 16 Sep 2009 13:09:24 +0900
mummer (3.20-3) unstable; urgency=low
Modified: trunk/packages/mummer/trunk/debian/control
===================================================================
--- trunk/packages/mummer/trunk/debian/control 2009-09-15 13:22:54 UTC (rev 3972)
+++ trunk/packages/mummer/trunk/debian/control 2009-09-16 05:21:00 UTC (rev 3973)
@@ -5,7 +5,7 @@
DM-Upload-Allowed: yes
Uploaders: Steffen Moeller <moeller at debian.org>, Andreas Tille <tille at debian.org>, Charles Plessy <plessy at debian.org>
Build-Depends: quilt, debhelper (>= 7.0.50), texlive-latex-base, texlive-latex-recommended, texlive-fonts-recommended
-Standards-Version: 3.8.2
+Standards-Version: 3.8.3
Homepage: http://mummer.sourceforge.net/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mummer/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mummer/trunk/
Modified: trunk/packages/mummer/trunk/debian/copyright
===================================================================
--- trunk/packages/mummer/trunk/debian/copyright 2009-09-15 13:22:54 UTC (rev 3972)
+++ trunk/packages/mummer/trunk/debian/copyright 2009-09-16 05:21:00 UTC (rev 3973)
@@ -2,18 +2,28 @@
Name : MUMmer
Contact : mummer-help at lists.sourceforge.net
-Source : http://www.mirrorservice.org/sites/download.sourceforge.net/pub/sourceforge/m/mu/mummer/MUMmer3.21.tar.gz
+Source : http://jaist.dl.sourceforge.net/project/mummer/mummer/3.22/MUMmer3.22.tar.gz
+Copyright : © 2003 by Stefan Kurtz and The Institute for Genomic Research.
License : Artistic
+
+Copyright : © 1999 by The Institute for Genomic Research.
+License : Artistic
+Comment :
+ MUMmer 1.0 code and documentation are copyright (c) 1999 by The Institute
+ for Genomic Research. The principle architect for the system was
+ Arthur Delcher.
+
+License : Artistic
This program is free software; you can redistribute it and/or modify it
under the terms of the "Artistic License" which comes with Debian.
-
- THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
- WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
+
+ THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
+ WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-On Debian systems, the complete text of the Artistic License
+On Debian systems, the complete text of the Artistic License
can be found in ‘/usr/share/common-licenses/Artistic’.
The Debian packaging is (C) 2005-2007, Steffen Moeller <moeller at inb.uni-luebeck.de>,
Deleted: trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff 2009-09-15 13:22:54 UTC (rev 3972)
+++ trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff 2009-09-16 05:21:00 UTC (rev 3973)
@@ -1,64 +0,0 @@
-Description: Dynamically allocates space for the strings, instead allocating a predefined size.
- See http://lists.debian.org/msgid-search/20090704120642.GH6047@kunpuu.plessy.org and its replies.
-Origin: vendor : Debian
-Bug: https://sourceforge.net/support/tracker.php?aid=1215086
-Index: ./src/tigr/annotate.cc
-===================================================================
---- ./src/tigr/annotate.cc
-+++ ./src/tigr.orig/annotate.cc
-@@ -10,6 +10,7 @@
- */
-
- #include "tigrinc.hh"
-+#include <assert.h>
-
- #define FIELD_LEN 20
- #define MAX_ALIGN 10000
-@@ -138,19 +139,26 @@ void Show_Alignment (char A [], long in
- // Print the alignment between strings A [1 .. M] and B [1 .. N] .
-
- {
-- static int D [MAX_ALIGN] [MAX_ALIGN];
-- static char Op [MAX_ALIGN] [MAX_ALIGN];
-- static char Show_A [2 * MAX_ALIGN];
-- static char Show_B [2 * MAX_ALIGN];
-+ int **D, *D_buf;
-+ char **Op, *Op_buf;
-+ char *Show_A;
-+ char *Show_B;
- int Errors, Tmp;
- long int i, j, Ct;
-
-- if (M >= MAX_ALIGN || N >= MAX_ALIGN)
-- {
-- printf ("\n *** Too long ***\n\n");
-- fprintf (Gaps_With_Errors_File, "%s %7s\n", Line, "-");
-- return;
-- }
-+ assert ( SIZE_MAX / (M+1) >= (N+1) ) ;
-+ D_buf = (int *) calloc ( (M+1)*(N+1), sizeof(int) ) ;
-+ assert ( D_buf ) ;
-+ D = &D_buf ;
-+ Op_buf = (char *) calloc ( (M+1)*(N+1), sizeof(char) ) ;
-+ assert ( Op_buf ) ;
-+ Op = &Op_buf ;
-+
-+ assert ( SIZE_MAX >> 1 >= (M+1) ) ;
-+ Show_A = (char *) calloc ( 2*(M+1) , sizeof(char) ) ;
-+ assert ( Show_A ) ;
-+ Show_B = (char *) calloc ( 2*(N+1) , sizeof(char) ) ;
-+ assert ( Show_B ) ;
-
- D [0] [0] = 0;
- Op [0] [0] = 'a';
-@@ -229,5 +237,10 @@ void Show_Alignment (char A [], long in
- putchar ('\n');
- Ct -= WIDTH;
- } while (Ct > 0);
-+
-+ free ( D_buf ) ;
-+ free ( Op_buf ) ;
-+ free ( Show_A ) ;
-+ free ( Show_B ) ;
- return;
- }
Modified: trunk/packages/mummer/trunk/debian/patches/02at_docs_web.diff
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/02at_docs_web.diff 2009-09-15 13:22:54 UTC (rev 3972)
+++ trunk/packages/mummer/trunk/debian/patches/02at_docs_web.diff 2009-09-16 05:21:00 UTC (rev 3973)
@@ -1,47 +1,47 @@
Description: Some PDFs were removed and have to be downloaded from the upstream website instead.
Origin: vendor : Debian
Forwarded: not-needed
---- ./docs/web/index.html.orig 2009-06-29 19:33:23.000000000 +0900
-+++ ./docs/web/index.html 2009-06-29 19:34:37.000000000 +0900
+--- mummer-3.22~dfsg.orig/docs/web/index.html
++++ mummer-3.22~dfsg/docs/web/index.html
@@ -25,11 +25,11 @@
- detect similarity, then the PROmer program can generate alignments
- based upon the six-frame translations of both input sequences. The
- original MUMmer system, version 1.0, is described in our <a
-- href=MUMmer.pdf>1999 <em>Nucleic Acids Research</em> paper</a>.
-+ href=http://mummer.sourceforge.net/MUMmer.pdf>1999 <em>Nucleic Acids Research</em> paper</a>.
- Version 2.1 appeared a few years later and is described in our <a
-- href=MUMmer2.pdf>2002 <em>Nucleic Acids Research</em> paper</a>,
-+ href=http://mummer.sourceforge.net/MUMmer2.pdf>2002 <em>Nucleic Acids Research</em> paper</a>,
- while MUMmer 3.0 was recently described in our <a
-- href=MUMmer3.pdf>2004 <em>Genome Biology</em> paper</a>. For more
-+ href=http://mummer.sourceforge.net/MUMmer3.pdf>2004 <em>Genome Biology</em> paper</a>. For more
- information regarding the MUMmer package, please refer to the:</p>
-
- <big><b><a
+ detect similarity, then the PROmer program can generate alignments
+ based upon the six-frame translations of both input sequences. The
+ original MUMmer system, version 1.0, is described in our <a
+- href=MUMmer.pdf>1999 <em>Nucleic Acids Research</em> paper</a>.
++ href=http://mummer.sourceforge.net/MUMmer.pdf>1999 <em>Nucleic Acids Research</em> paper</a>.
+ Version 2.1 appeared a few years later and is described in our <a
+- href=MUMmer2.pdf>2002 <em>Nucleic Acids Research</em> paper</a>,
++ href=http://mummer.sourceforge.net/MUMmer2.pdf>2002 <em>Nucleic Acids Research</em> paper</a>,
+ while MUMmer 3.0 was recently described in our <a
+- href=MUMmer3.pdf>2004 <em>Genome Biology</em> paper</a>. For more
++ href=http://mummer.sourceforge.net/MUMmer3.pdf>2004 <em>Genome Biology</em> paper</a>. For more
+ information regarding the MUMmer package, please refer to the:</p>
+
+ <big><b><a
@@ -172,7 +172,7 @@
- <h3><em><font color="#CC0000"> Applications </font></em></h3>
- <p>MUMmer 1 was used to detect numerous large-scale inversions in
- bacterial genomes, leading to a new model of chromosome
-- inversions, reported in this <a href=XFiles.pdf>2000 <em>Genome
-+ inversions, reported in this <a href=http://mummer.sourceforge.net/XFiles.pdf>2000 <em>Genome
- Biology</em> paper</a>. It was also used to discover evidence for
- a recent whole-genome duplication in <em>Arabidopsis
- thaliana</em>, reported in "Analysis of the genome sequence of the
+ <h3><em><font color="#CC0000"> Applications </font></em></h3>
+ <p>MUMmer 1 was used to detect numerous large-scale inversions in
+ bacterial genomes, leading to a new model of chromosome
+- inversions, reported in this <a href=XFiles.pdf>2000 <em>Genome
++ inversions, reported in this <a href=http://mummer.sourceforge.net/XFiles.pdf>2000 <em>Genome
+ Biology</em> paper</a>. It was also used to discover evidence for
+ a recent whole-genome duplication in <em>Arabidopsis
+ thaliana</em>, reported in "Analysis of the genome sequence of the
@@ -227,14 +227,14 @@
- <p><a href="manual">MUMmer 3 user manual</a></p>
- <p><a href="examples">MUMmer 3 examples</a></p>
- <p>Open source MUMmer 3.0 is described in "<a
-- href=MUMmer3.pdf>Versatile and open software for comparing large genomes</a>."
-+ href=http://mummer.sourceforge.net/MUMmer3.pdf>Versatile and open software for comparing large genomes</a>."
- S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu,
- and S.L. Salzberg, <em>Genome Biology</em> (2004), 5:R12.</p>
-- <p>MUMmer 2.1, NUCmer, and PROmer are described in "<a href=MUMmer2.pdf>Fast
-+ <p>MUMmer 2.1, NUCmer, and PROmer are described in "<a href=http://mummer.sourceforge.net/MUMmer2.pdf>Fast
- Algorithms for Large-scale Genome Alignment and Comparision</a>." A.L. Delcher,
- A. Phillippy, J. Carlton, and S.L. Salzberg, <em>Nucleic Acids Research</em>
- (2002), Vol. 30, No. 11 2478-2483.</p>
-- <p>MUMmer 1.0 is described in "<a href=MUMmer.pdf>Alignment of Whole Genomes</a>."
-+ <p>MUMmer 1.0 is described in "<a href=http://mummer.sourceforge.net/MUMmer.pdf>Alignment of Whole Genomes</a>."
- A.L. Delcher, S. Kasif, R.D. Fleischmann, J. Peterson, O. White, and S.L.
- Salzberg, <em>Nucleic Acids Research</em>, 27:11 (1999), 2369-2376.</p>
- <p>Space efficent suffix trees are described in "<a
+ <p><a href="manual">MUMmer 3 user manual</a></p>
+ <p><a href="examples">MUMmer 3 examples</a></p>
+ <p>Open source MUMmer 3.0 is described in "<a
+- href=MUMmer3.pdf>Versatile and open software for comparing large genomes</a>."
++ href=http://mummer.sourceforge.net/MUMmer3.pdf>Versatile and open software for comparing large genomes</a>."
+ S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu,
+ and S.L. Salzberg, <em>Genome Biology</em> (2004), 5:R12.</p>
+- <p>MUMmer 2.1, NUCmer, and PROmer are described in "<a href=MUMmer2.pdf>Fast
++ <p>MUMmer 2.1, NUCmer, and PROmer are described in "<a href=http://mummer.sourceforge.net/MUMmer2.pdf>Fast
+ Algorithms for Large-scale Genome Alignment and Comparision</a>." A.L. Delcher,
+ A. Phillippy, J. Carlton, and S.L. Salzberg, <em>Nucleic Acids Research</em>
+ (2002), Vol. 30, No. 11 2478-2483.</p>
+- <p>MUMmer 1.0 is described in "<a href=MUMmer.pdf>Alignment of Whole Genomes</a>."
++ <p>MUMmer 1.0 is described in "<a href=http://mummer.sourceforge.net/MUMmer.pdf>Alignment of Whole Genomes</a>."
+ A.L. Delcher, S. Kasif, R.D. Fleischmann, J. Peterson, O. White, and S.L.
+ Salzberg, <em>Nucleic Acids Research</em>, 27:11 (1999), 2369-2376.</p>
+ <p>Space efficent suffix trees are described in "<a
Modified: trunk/packages/mummer/trunk/debian/patches/series
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/series 2009-09-15 13:22:54 UTC (rev 3972)
+++ trunk/packages/mummer/trunk/debian/patches/series 2009-09-16 05:21:00 UTC (rev 3973)
@@ -1,2 +1 @@
-01sm_src_tigr.diff
02at_docs_web.diff
Added: trunk/packages/mummer/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/mummer/trunk/debian/upstream-metadata.yaml (rev 0)
+++ trunk/packages/mummer/trunk/debian/upstream-metadata.yaml 2009-09-16 05:21:00 UTC (rev 3973)
@@ -0,0 +1,19 @@
+DOI: 10.1186/gb-2004-5-2-r12
+Homepage: http://mummer.sourceforge.net/
+PubMed: 14759262
+Reference: |
+ @Article{14759262,
+ AUTHOR = {Kurtz, Stefan and Phillippy, Adam and Delcher, Arthur and Smoot, Michael and Shumway, Martin and Antonescu, Corina and Salzberg, Steven},
+ TITLE = {Versatile and open software for comparing large genomes},
+ JOURNAL = {Genome Biology},
+ VOLUME = {5},
+ YEAR = {2004},
+ NUMBER = {2},
+ PAGES = {R12},
+ URL = {http://genomebiology.com/2004/5/2/R12},
+ DOI = {10.1186/gb-2004-5-2-r12},
+ PubMedID = {14759262},
+ ISSN = {1465-6906},
+ }
+Repository: http://mummer.cvs.sourceforge.net/mummer/
+Screenshots: http://sourceforge.net/project/screenshots.php?group_id=133157
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